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Table 1 Migraine-associated single nucleotide polymorphisms and the molecular pathways they are linked to

From: Novel hypotheses emerging from GWAS in migraine?

Genomic regiona Index
SNPb
Secondary
SNPc
Gene nearest index SNP Genes overlapping credible SNPs Genes prioritised with DEPICT Pathways identified with g:GOSt tool
1 rs10218452   PRDM16 PRDM16 PRDM16 Vascular function; Metal ion homeostasis
   rs12135062     
2 rs1572668   LRRIQ3    
3 rs2078371   TSPAN2   NGF  
   rs7544256     
4 rs6693567   ADAMTSL4 RPRD2 ECM1 Vascular function
5 rs1925950   MEF2D MEF2D   Vascular function
6 rs138556413   CARF CARF NBEAL1  
7 rs10166942   TRPM8 TRPM8   Ion channel activity
   rs566529     
8 rs6791480   TGFBR2   TGFBR2 Vascular function; Metal ion homeostasis
9 rs13078967   GPR149   ARHGEF26 Vascular function
10 rs7684253   SPINK2   REST Vascular function; Metal ion homeostasis; Ion channel activity
11 rs9349379   PHACTR1 PHACTR1   Vascular function
12 rs140002913   NOTCH4    
13 rs10456100   KCNK5 KCNK5   Ion channel activity
14 rs67338227   FHL5 FHL5   Vascular function
   rs4839827     
15 rs28455731   GJA1   GJA1 Vascular function
16 rs1268083   HEY2 HEY2, NCOA7 HEY2 Vascular function
17 rs186166891   SUGCT SUGCT   
18 rs10155855   DOCK4    
19 rs6478241   ASTN2 ASTN2   
20 rs2506142   NRP1 NRP1 NRP1 Vascular function; Metal ion homeostasis
21 rs10786156   PLCE1 PLCE1 PLCE1 Vascular function
   rs75473620     
22 rs12260159   HPSE2 HPSE2 HPSE2  
23 rs2223089   ARMS2 PLEKHA1, HTRA1 HTRA1 Vascular function
24 rs4910165   MRVI1 MRVI1 MRVI1  
25 rs11031122   MPPED2 MPPED2   
26 rs10895275   YAP1 YAP1 YAP1 Vascular function
27 rs561561   IGSF9B IGSF9B   
28 rs1024905   FGF6   FGF6 Vascular function
29 rs11172113   LRP1 LRP1 LRP1 Vascular function; Metal ion homeostasis
   rs11172055     
30 rs11624776   ITPK1    
31 rs77505915   CFDP1 CFDP1, TMEM170A   
32 rs4081947   ZCCHC14   ZCCHC14 Vascular function; Metal ion homeostasis
33 rs75213074   WSCD1    
34 rs17857135   RNF213 RNF213   Metal ion homeostasis
35 rs111404218   JAG1   JAG1 Vascular function; Metal ion homeostasis
36 rs4814864   SLC24A3 SLC24A3   Ion channel activity
37 rs144017103   CCM2L CCM2L CCM2L Vascular function
38 rs12845494   MED14    
  1. aGenomic region is an independent genomic region (> 250 kb apart) that harbours at least one migraine risk SNP; bIndex SNP is the SNP with the lowest p-value at a genomic region. cSecondary SNP is a genome-wide significant SNP that is not in linkage disequilibrium with the index SNP. Associations were identified for the migraine without aura subtype. DEPICT, data-driven expression-prioritized integration for complex traits; g:GOSt tool refers to web-based gene functional profiling software g:Profiler128 (http://biit.cs.ut.ee/gprofiler/) (depicted are only the more prominent pathways vascular function, metal ion homeostasis, ion channel activity pathways) (Compiled and adapted from [17, 33])
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